This notebook is for performing downstream analysis of CYCLOPS. It includes running cosinor regression and assessing differential rhythmicity (two ways for both), calling the enrichR API via python, using fgsea in R, running PSEA, outputing files for making KEGG map diagrams, etc.

Load Packages

This notebook makes use of python via anaconda. Please make sure you install anaconda to proceed:

conda_list()

Select your conda environment of choice, in my case, item 2 from list above:

conda_list()[[2]][2] %>% 
  use_condaenv(required = TRUE)
Warning: Previous request to `use_python("/usr/bin/python3", required = TRUE)` will be ignored. It is superseded by request to `use_python("/Users/henryhollis/opt/anaconda3/bin/python")
print(paste("Using cond env:",conda_list()[[1]][2] ))
[1] "Using cond env: base"

Setup

Select the CYCLOPS ordering path and path to data file and path to DEseq2 differential expression results:

#path to cyclops ordering
path_to_cyclops_ordering = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/"

#path to normalized counts
path_to_tmm_file = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/tmms/scROSMAP/cogdx_controls/EdgeR_filt_normed/Microglia_4_5_6_7_8_10_11_13_15_16_FiltByExprDefault_TMM.csv"

# optional path to file containing differential expression results
deseq_de_filename = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/simple_differential_expr/Mglia_4_5_6_7_8_10_11_13_15_16/ Microglia_4_5_6_7_8_10_11_13_15_16_filtByExpr_combatSeq_edgeR_DE_exactTest.csv"

path_to_rosmap_clin = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Meta_data/cleaned_rosmap_meta_cogdxConds.csv"
metabolon_filename = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Brain514_assay_data.csv"
metabolon_datakey = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Data_Dictionary.csv"

#BHQ corrected p cutoff to be considered cycling in analysis:
isCyclingBHQCutoff = 0.1
percentile = 0.025
useBatch = T

Cosinor Regression and Differential Rhythmicity

Run cosinor regression and differential rhythmicity analysis with custom script and with compareRhythms library. I make use of Ensembl and Entrez IDs so I need the following translation dictionaries:

# read in translation dict between gene symbols and other alias
Ensembl_dict = readxl::read_xlsx("scROSMAP_ENSEMBL_dict.xlsx")

#run custom cycling and differential rhythmicity analysis
print("***Running cosinor and differential rhythms analysis***")
[1] "***Running cosinor and differential rhythms analysis***"
run_cycling_and_dr_analysis(path_to_cyclops_ordering, path_to_tmm_file, isCyclingSigCutoff = isCyclingBHQCutoff, percentile = percentile, useBatch = useBatch)

Running is_cycling() on cond_subset: cond_0
NOTE: Using batches in regression.

[>----------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%

Running is_cycling() on cond_subset: cond_1
NOTE: Using batches in regression.

[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%

Running is_cycling_method2() (analogue of compareRhythms) on all subjects
NOTE: Using batches in regression.

[>----------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%

Running Mesor_differences()
NOTE: Using batches in regression.

[>----------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running diff_rhyth_AD_severity()
NOTE: Using batches in regression.
Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.

Running diff_rhyth() on seedlist of size: 282
NOTE: Using batches in regression.

[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running diff_rhyth() on seedlist of size: 110
NOTE: Using batches in regression.

[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[===============================================================>-------------------------------------------------------------------------]  46%
[================================================================>------------------------------------------------------------------------]  47%
[=================================================================>-----------------------------------------------------------------------]  48%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[============================================================================>------------------------------------------------------------]  56%
[=============================================================================>-----------------------------------------------------------]  57%
[===============================================================================>---------------------------------------------------------]  58%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[==========================================================================================>----------------------------------------------]  66%
[===========================================================================================>---------------------------------------------]  67%
[============================================================================================>--------------------------------------------]  68%
[==============================================================================================>------------------------------------------]  69%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[========================================================================================================>--------------------------------]  76%
[=========================================================================================================>-------------------------------]  77%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[=============================================================================================================>---------------------------]  80%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  83%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[=====================================================================================================================>-------------------]  86%
[=======================================================================================================================>-----------------]  87%
[========================================================================================================================>----------------]  88%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  90%
[============================================================================================================================>------------]  91%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  94%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[===================================================================================================================================>-----]  96%
[====================================================================================================================================>----]  97%
[======================================================================================================================================>--]  98%
[=======================================================================================================================================>-]  99%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running diff_rhyth() on seedlist of size: 3130
NOTE: Using batches in regression.

[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running diff_rhyth() on seedlist of size: 301
NOTE: Using batches in regression.

[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running diff_rhyth() on seedlist of size: 3184
NOTE: Using batches in regression.

[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Plotting

With custom regression, I have to remake clock face plots, genes plots, etc.

setwd(path_to_cyclops_ordering)
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
if (!(dir.exists("downstream_output/plots"))){
  dir.create("downstream_output/plots")
}

#for cycling_in_CTL.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/CTL_clock_face_plot.png"), "downstream_output/cosinor_results_CTL.csv", mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0, force_align = 5.907, force_flipped = T)
[1] "Shifting phases using `force align`"
[1] "flipping acrophases."
NULL
setwd(path_to_cyclops_ordering)

#for cycling_in_AD.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/AD_clock_face_plot.png"),"downstream_output/cosinor_results_AD.csv",mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0, force_align = 5.907, force_flipped = T)
[1] "Shifting phases using `force align`"
[1] "flipping acrophases."
NULL
#plot cyclops histogram
plot_subject_histogram(path_to_cyclops_ordering, "cond_0")
null device 
          1 
plot_subject_histogram(path_to_cyclops_ordering, "cond_1")
null device 
          1 
#Gene Tracings
plot_core_clock_genes(path_to_tmm_file, path_to_cyclops_ordering, useBatch = useBatch, percentile = percentile, split_cond_plots = T)
[1] "NOTE: Using batches in plotting"

Plot Other Genes

plot_me = c("RPL18","RPS7","RPL22","RPS18","RPL8","RPL10A","RPS13","RPL14","RPS15A","RPS12","RPL36AL","RPL34","RPL30","RPL9","RPL21","RPS28","RPSA","RPL26","RPL27A","FAU","RPS3A","RPL7A","RPL17","RPS27A","RPS16","RPL15","RPLP1","RPL7","RPL10","RPL23A","RPL18A","RPL3","RPL12","RPL39","RPL37A","RPL37","RPS10","RPL13","RPL35A","RPS23","RPL13A","RPL38","RPS29","RPL24","RPL41","RPL35","RPS26","RPS2","RPS9","RPL32","RPL6","RPS21","RPS24","RPS25","RPL36","RPL19","RPS27","RPL29","RPS15","RPS3","RPS5","RPS8","RPL27","RSL24D1","RPS6","RPL11")

tmm = read_csv(path_to_tmm_file, show_col_types = FALSE)
  cyc_pred_file = list.files(path = paste0(path_to_cyclops_ordering, "/Fits/"), pattern = '*Fit_Output_*')
cyc_pred = read_csv(paste(path_to_cyclops_ordering, "Fits", cyc_pred_file[1], sep = '/'), show_col_types = FALSE)
plot_gene_trace(cyc_pred, tmm, plot_me , percentile = percentile, useBatch = useBatch)
[1] "NOTE: Using batches in plotting"

EnrichR

Call EnrichR API with python, supplying various lists from cycling and differential rhythm analysis.

path = getwd()
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)
#create list of filenames from the enrichR_files subfolder
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|diff_mesor)")

#run system command to call python script that uses enrichR API
sapply(gene_lists, function(x){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"enrichR_files/EnrichR_background.csv\""))})
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/AD_CTL_mthd2_cyclers_AR25BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/AD_CTL_mthd2_cyclers_AR25BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 301):
           Ensembl Gene_Symbols
0  ENSG00000142920        AZIN2
1  ENSG00000132639       SNAP25
2  ENSG00000168329       CX3CR1
3  ENSG00000166833         NAV2
4  ENSG00000213316        LTC4S
Background DataFrame (nrow: 6966):
           Ensembl Gene_Symbols
0  ENSG00000078808         SDF4
1  ENSG00000160087       UBE2J2
2  ENSG00000131584        ACAP3
3  ENSG00000127054       INTS11
4  ENSG00000175756     AURKAIP1
Directory "EnrichR_results/EnrichR_ADCTLmthd2cyclersAR25BHQ1_BCKGRND-EnrichRbackground" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/AD_cyclers_AR25BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/AD_cyclers_AR25BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 197):
           Ensembl Gene_Symbols
0  ENSG00000132639       SNAP25
1  ENSG00000142920        AZIN2
2  ENSG00000017427         IGF1
3  ENSG00000166833         NAV2
4  ENSG00000213316        LTC4S
Background DataFrame (nrow: 6966):
           Ensembl Gene_Symbols
0  ENSG00000078808         SDF4
1  ENSG00000160087       UBE2J2
2  ENSG00000131584        ACAP3
3  ENSG00000127054       INTS11
4  ENSG00000175756     AURKAIP1
Directory "EnrichR_results/EnrichR_ADcyclersAR25BHQ1_BCKGRND-EnrichRbackground" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/AD_cyclers_AR33BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/AD_cyclers_AR33BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 80):
           Ensembl Gene_Symbols
0  ENSG00000142920        AZIN2
1  ENSG00000017427         IGF1
2  ENSG00000166833         NAV2
3  ENSG00000213316        LTC4S
4  ENSG00000019485       PRDM11
Background DataFrame (nrow: 6966):
           Ensembl Gene_Symbols
0  ENSG00000078808         SDF4
1  ENSG00000160087       UBE2J2
2  ENSG00000131584        ACAP3
3  ENSG00000127054       INTS11
4  ENSG00000175756     AURKAIP1
Directory "EnrichR_results/EnrichR_ADcyclersAR33BHQ1_BCKGRND-EnrichRbackground" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/CTL_cyclers_AR25BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/CTL_cyclers_AR25BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 204):
           Ensembl Gene_Symbols
0  ENSG00000168329       CX3CR1
1  ENSG00000142920        AZIN2
2  ENSG00000196683        TOMM7
3  ENSG00000070087         PFN2
4  ENSG00000166833         NAV2
Background DataFrame (nrow: 6966):
           Ensembl Gene_Symbols
0  ENSG00000078808         SDF4
1  ENSG00000160087       UBE2J2
2  ENSG00000131584        ACAP3
3  ENSG00000127054       INTS11
4  ENSG00000175756     AURKAIP1
Directory "EnrichR_results/EnrichR_CTLcyclersAR25BHQ1_BCKGRND-EnrichRbackground" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/CTL_cyclers_AR33BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/CTL_cyclers_AR33BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 74):
           Ensembl Gene_Symbols
0  ENSG00000168329       CX3CR1
1  ENSG00000142920        AZIN2
2  ENSG00000166833         NAV2
3  ENSG00000019485       PRDM11
4  ENSG00000213316        LTC4S
Background DataFrame (nrow: 6966):
           Ensembl Gene_Symbols
0  ENSG00000078808         SDF4
1  ENSG00000160087       UBE2J2
2  ENSG00000131584        ACAP3
3  ENSG00000127054       INTS11
4  ENSG00000175756     AURKAIP1
Directory "EnrichR_results/EnrichR_CTLcyclersAR33BHQ1_BCKGRND-EnrichRbackground" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/diff_mesor_all_genes_BHQ05.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/diff_mesor_all_genes_BHQ05.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 34):
           Ensembl Gene_Symbols
0  ENSG00000188641         DPYD
1  ENSG00000152689      RASGRP3
2  ENSG00000121964        GTDC1
3  ENSG00000116117       PARD3B
4  ENSG00000131389       SLC6A6
Background DataFrame (nrow: 6966):
           Ensembl Gene_Symbols
0  ENSG00000078808         SDF4
1  ENSG00000160087       UBE2J2
2  ENSG00000131584        ACAP3
3  ENSG00000127054       INTS11
4  ENSG00000175756     AURKAIP1
Directory "EnrichR_results/EnrichR_diffmesorallgenesBHQ05_BCKGRND-EnrichRbackground" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
AD_CTL_mthd2_cyclers_AR25BHQ1.csv           AD_cyclers_AR25BHQ1.csv           AD_cyclers_AR33BHQ1.csv          CTL_cyclers_AR25BHQ1.csv 
                                0                                 0                                 0                                 0 
         CTL_cyclers_AR33BHQ1.csv    diff_mesor_all_genes_BHQ05.csv 
                                0                                 0 
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

setwd("enrichR_files/")
all_DR_gene_lists = list.files( pattern = "^(DR_)")
method2_files = grepl("mthd2", all_DR_gene_lists)
DR_gene_lists_method1 = all_DR_gene_lists[!method2_files]
DR_backgrounds_method1 = paste0("diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method1, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists_method2 = all_DR_gene_lists[method2_files]
DR_backgrounds_method2 = paste0("diff_rhythms_method2_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method2, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists = c(DR_gene_lists_method1, DR_gene_lists_method2)
DR_backgrounds = c(DR_backgrounds_method1, DR_backgrounds_method2)

# repeat with differential gene lists
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
mapply(function(x, y){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"",y , "\""))},
  DR_gene_lists, 
  DR_backgrounds)
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 12):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000136715       SAP130  ...  0.409230             0.238614
1  ENSG00000127990         SGCE  ...  1.000000             0.866906
2  ENSG00000164985        PSIP1  ...  0.958730             2.777088
3  ENSG00000119414        PPP6C  ...  1.000000             1.002309
4  ENSG00000148606       POLR3A  ...  0.498371             0.654147

[5 rows x 10 columns]
Background DataFrame (nrow: 3130):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000131584        ACAP3  0.669440  ...  0.861040   1.0            -0.772190
1  ENSG00000175756     AURKAIP1  0.526738  ...  0.796164   1.0             0.185463
2  ENSG00000142609       CFAP74  0.238942  ...  0.629488   1.0            -0.349632
3  ENSG00000187730        GABRD  0.490882  ...  0.786366   1.0             0.532005
4  ENSG00000158109       TPRG1L  0.834309  ...  0.933889   1.0            -0.279667

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio1" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 7):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000148219        ASTN2  ...  0.127360             1.276032
1  ENSG00000140470     ADAMTS17  ...  0.066427             2.177640
2  ENSG00000158258       CLSTN2  ...  0.517345            -0.586008
3  ENSG00000095261        PSMD5  ...  0.368817             1.203439
4  ENSG00000134419       RPS15A  ...  0.431026            -1.276418

[5 rows x 10 columns]
Background DataFrame (nrow: 282):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000097021        ACOT7  0.009033  ...  0.282688   1.0             1.408467
1  ENSG00000171680      PLEKHG5  0.086548  ...  0.488133   1.0             0.943269
2  ENSG00000049246         PER3  0.252187  ...  0.700387   1.0             0.326548
3  ENSG00000028137     TNFRSF1B  0.357533  ...  0.741148   1.0             0.499864
4  ENSG00000173436      MICOS10  0.628646  ...  0.864771   1.0             0.217262

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio33.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio33.csv
Background DataFrame (nrow: 2):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000140470     ADAMTS17  ...  0.025911             2.177640
1  ENSG00000269893        SNHG8  ...  0.286194            -1.126985

[2 rows x 10 columns]
Background DataFrame (nrow: 110):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000049246         PER3  0.252187  ...  0.777778   1.0             0.326548
1  ENSG00000130775      THEMIS2  0.705588  ...  0.949272   1.0             0.371321
2  ENSG00000142920        AZIN2  0.356249  ...  0.777778   1.0             0.223556
3  ENSG00000132122       SPATA6  0.240131  ...  0.777778   1.0             0.237122
4  ENSG00000162645         GBP2  0.370574  ...  0.777778   1.0             0.647551

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersCyclingBHQ1AR33DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio33" created.
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 12):
           Ensembl Gene_Symbols
0  ENSG00000136715       SAP130
1  ENSG00000127990         SGCE
2  ENSG00000164985        PSIP1
3  ENSG00000148219        ASTN2
4  ENSG00000119414        PPP6C
Background DataFrame (nrow: 3130):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000131584        ACAP3  0.669440  ...  0.861040   1.0            -0.772190
1  ENSG00000175756     AURKAIP1  0.526738  ...  0.796164   1.0             0.185463
2  ENSG00000142609       CFAP74  0.238942  ...  0.629488   1.0            -0.349632
3  ENSG00000187730        GABRD  0.490882  ...  0.786366   1.0             0.532005
4  ENSG00000158109       TPRG1L  0.834309  ...  0.933889   1.0            -0.279667

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio1" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 4):
           Ensembl Gene_Symbols
0  ENSG00000136261         BZW2
1  ENSG00000148219        ASTN2
2  ENSG00000095261        PSMD5
3  ENSG00000140470     ADAMTS17
Background DataFrame (nrow: 282):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000097021        ACOT7  0.009033  ...  0.282688   1.0             1.408467
1  ENSG00000171680      PLEKHG5  0.086548  ...  0.488133   1.0             0.943269
2  ENSG00000049246         PER3  0.252187  ...  0.700387   1.0             0.326548
3  ENSG00000028137     TNFRSF1B  0.357533  ...  0.741148   1.0             0.499864
4  ENSG00000173436      MICOS10  0.628646  ...  0.864771   1.0             0.217262

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25" created.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio33.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio33.csv
Background DataFrame (nrow: 1):
           Ensembl Gene_Symbols
0  ENSG00000140470     ADAMTS17
Background DataFrame (nrow: 110):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000049246         PER3  0.252187  ...  0.777778   1.0             0.326548
1  ENSG00000130775      THEMIS2  0.705588  ...  0.949272   1.0             0.371321
2  ENSG00000142920        AZIN2  0.356249  ...  0.777778   1.0             0.223556
3  ENSG00000132122       SPATA6  0.240131  ...  0.777778   1.0             0.237122
4  ENSG00000162645         GBP2  0.370574  ...  0.777778   1.0             0.647551

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR33DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio33" created.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 0):
Empty DataFrame
Columns: [Ensembl, Gene_Symbols]
Index: []
Background DataFrame (nrow: 3130):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000131584        ACAP3  0.669440  ...  0.861040   1.0            -0.772190
1  ENSG00000175756     AURKAIP1  0.526738  ...  0.796164   1.0             0.185463
2  ENSG00000142609       CFAP74  0.238942  ...  0.629488   1.0            -0.349632
3  ENSG00000187730        GABRD  0.490882  ...  0.786366   1.0             0.532005
4  ENSG00000158109       TPRG1L  0.834309  ...  0.933889   1.0            -0.279667

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRlostAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio1" created.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 3):
           Ensembl Gene_Symbols
0  ENSG00000158258       CLSTN2
1  ENSG00000269893        SNHG8
2  ENSG00000134419       RPS15A
Background DataFrame (nrow: 282):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000097021        ACOT7  0.009033  ...  0.282688   1.0             1.408467
1  ENSG00000171680      PLEKHG5  0.086548  ...  0.488133   1.0             0.943269
2  ENSG00000049246         PER3  0.252187  ...  0.700387   1.0             0.326548
3  ENSG00000028137     TNFRSF1B  0.357533  ...  0.741148   1.0             0.499864
4  ENSG00000173436      MICOS10  0.628646  ...  0.864771   1.0             0.217262

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRlostAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio33.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio33.csv
Background DataFrame (nrow: 1):
           Ensembl Gene_Symbols
0  ENSG00000269893        SNHG8
Background DataFrame (nrow: 110):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000049246         PER3  0.252187  ...  0.777778   1.0             0.326548
1  ENSG00000130775      THEMIS2  0.705588  ...  0.949272   1.0             0.371321
2  ENSG00000142920        AZIN2  0.356249  ...  0.777778   1.0             0.223556
3  ENSG00000132122       SPATA6  0.240131  ...  0.777778   1.0             0.237122
4  ENSG00000162645         GBP2  0.370574  ...  0.777778   1.0             0.647551

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRlostAmpADCyclingBHQ1AR33DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio33" created.
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 12):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000136715       SAP130  ...  0.416290             0.238614
1  ENSG00000127990         SGCE  ...  1.000000             0.866906
2  ENSG00000164985        PSIP1  ...  0.975270             2.777088
3  ENSG00000119414        PPP6C  ...  1.000000             1.002309
4  ENSG00000148606       POLR3A  ...  0.506969             0.654147

[5 rows x 10 columns]
Background DataFrame (nrow: 3184):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000078808         SDF4  0.754184  ...  0.904053   1.0             0.300964
1  ENSG00000175756     AURKAIP1  0.526738  ...  0.806833   1.0             0.185463
2  ENSG00000242485       MRPL20  0.033929  ...  0.387206   1.0             0.258299
3  ENSG00000142609       CFAP74  0.238942  ...  0.638216   1.0            -0.349632
4  ENSG00000187730        GABRD  0.490882  ...  0.796315   1.0             0.532005

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersmthd2CyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio1" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 9):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000127990         SGCE  ...  0.097682             0.866906
1  ENSG00000148219        ASTN2  ...  0.135941             1.276032
2  ENSG00000140470     ADAMTS17  ...  0.070903             2.177640
3  ENSG00000095261        PSMD5  ...  0.393666             1.203439
4  ENSG00000134419       RPS15A  ...  0.460067            -1.276418

[5 rows x 10 columns]
Background DataFrame (nrow: 301):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000097021        ACOT7  0.009033  ...  0.247176   1.0             1.408467
1  ENSG00000171680      PLEKHG5  0.086548  ...  0.482427   1.0             0.943269
2  ENSG00000049246         PER3  0.252187  ...  0.706044   1.0             0.326548
3  ENSG00000028137     TNFRSF1B  0.357533  ...  0.758794   1.0             0.499864
4  ENSG00000173436      MICOS10  0.628646  ...  0.867992   1.0             0.217262

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersmthd2CyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py:177: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(2, 2, figsize=(15, 10))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 12):
           Ensembl Gene_Symbols
0  ENSG00000136715       SAP130
1  ENSG00000127990         SGCE
2  ENSG00000164985        PSIP1
3  ENSG00000148219        ASTN2
4  ENSG00000119414        PPP6C
Background DataFrame (nrow: 3184):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000078808         SDF4  0.754184  ...  0.904053   1.0             0.300964
1  ENSG00000175756     AURKAIP1  0.526738  ...  0.806833   1.0             0.185463
2  ENSG00000242485       MRPL20  0.033929  ...  0.387206   1.0             0.258299
3  ENSG00000142609       CFAP74  0.238942  ...  0.638216   1.0            -0.349632
4  ENSG00000187730        GABRD  0.490882  ...  0.796315   1.0             0.532005

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2gainAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio1" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
Saved TRRUST_Transcription_Factors_2019 results to file
Saved GO_Cellular_Component_2023 results to file
Saved TRANSFAC_and_JASPAR_PWMs results to file
Saved Transcription_Factor_PPIs results to file
Saved TargetScan_microRNA_2017 results to file
Saved miRTarBase_2017 results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 5):
           Ensembl Gene_Symbols
0  ENSG00000136261         BZW2
1  ENSG00000127990         SGCE
2  ENSG00000148219        ASTN2
3  ENSG00000095261        PSMD5
4  ENSG00000140470     ADAMTS17
Background DataFrame (nrow: 301):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000097021        ACOT7  0.009033  ...  0.247176   1.0             1.408467
1  ENSG00000171680      PLEKHG5  0.086548  ...  0.482427   1.0             0.943269
2  ENSG00000049246         PER3  0.252187  ...  0.706044   1.0             0.326548
3  ENSG00000028137     TNFRSF1B  0.357533  ...  0.758794   1.0             0.499864
4  ENSG00000173436      MICOS10  0.628646  ...  0.867992   1.0             0.217262

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2gainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25" created.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 0):
Empty DataFrame
Columns: [Ensembl, Gene_Symbols]
Index: []
Background DataFrame (nrow: 3184):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000078808         SDF4  0.754184  ...  0.904053   1.0             0.300964
1  ENSG00000175756     AURKAIP1  0.526738  ...  0.806833   1.0             0.185463
2  ENSG00000242485       MRPL20  0.033929  ...  0.387206   1.0             0.258299
3  ENSG00000142609       CFAP74  0.238942  ...  0.638216   1.0            -0.349632
4  ENSG00000187730        GABRD  0.490882  ...  0.796315   1.0             0.532005

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2lostAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio1" created.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 4):
           Ensembl Gene_Symbols
0  ENSG00000158258       CLSTN2
1  ENSG00000269893        SNHG8
2  ENSG00000196683        TOMM7
3  ENSG00000134419       RPS15A
Background DataFrame (nrow: 301):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000097021        ACOT7  0.009033  ...  0.247176   1.0             1.408467
1  ENSG00000171680      PLEKHG5  0.086548  ...  0.482427   1.0             0.943269
2  ENSG00000049246         PER3  0.252187  ...  0.706044   1.0             0.326548
3  ENSG00000028137     TNFRSF1B  0.357533  ...  0.758794   1.0             0.499864
4  ENSG00000173436      MICOS10  0.628646  ...  0.867992   1.0             0.217262

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2lostAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
         DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv         DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv         DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv 
                                            0                                             0                                             0 
       DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv       DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv       DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv 
                                            0                                             0                                             0 
       DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv       DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv       DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv 
                                            0                                             0                                             0 
   DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv   DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv  DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            0                                             0                                             0 
DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv  DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv 
                                            0                                             0                                             0 
#AD severity
system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/strong_cogdx_diffs_AR25.csv\" -b \"enrichR_files/AD_cyclers_AR25BHQ05.csv\""))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/strong_cogdx_diffs_AR25.csv', 'background_list_file': 'enrichR_files/AD_cyclers_AR25BHQ05.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/strong_cogdx_diffs_AR25.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/AD_cyclers_AR25BHQ05.csv
Background DataFrame (nrow: 0):
Empty DataFrame
Columns: [Ensembl, Gene_Symbols]
Index: []
File not found.
Traceback (most recent call last):
  File "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py", line 90, in <module>
    background = list(background_df['Gene_Symbols'])
TypeError: 'NoneType' object is not subscriptable

FGSEA

path = getwd()
setwd(path_to_cyclops_ordering)
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
if (!(dir.exists("downstream_output/fGSEA"))){
  dir.create("downstream_output/fGSEA")
  dir.create(paste("downstream_output", "fGSEA", "rnk_files", sep = "/"))
  dir.create(paste("downstream_output" , "fGSEA", "fGSEA_results", sep = "/"))
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#create rnk files
write_rnks(path_to_cyclops_ordering, isCyclingBHQCutoff_str)
[1] "Creating rnk files for fGSEA."
#path of parent folder
setwd(path)

#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_Gene_Symbol_with_Remapping_MSigDB.v2023.1.Hs.chip", sep = '\t')

setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))

rnk_files = list.files(pattern = ".rnk")


if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results", sep = "/")))){
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", sep = "/") )
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", "plots",sep = "/"))
}

run_fgsea(rnk_files, gene_remapping_dict, pathways)
[1] "../fGSEA_results/AD_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
Saving 7 x 7 in image
[1] "../fGSEA_results/CTL_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/differential_mesor_all_genes_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio1_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio1_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_minusLogPRanked_method2.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
                                           AD_cyclers_minusLogPRanked.rnk 
                  "../fGSEA_results/plots/AD_cyclers_minusLogPRanked.png" 
                                          CTL_cyclers_minusLogPRanked.rnk 
                 "../fGSEA_results/plots/CTL_cyclers_minusLogPRanked.png" 
                         differential_mesor_all_genes_minusLogPRanked.rnk 
"../fGSEA_results/plots/differential_mesor_all_genes_minusLogPRanked.png" 
                                   DRgenesAmpRatio1_Log(AD-CTL)ranked.rnk 
          "../fGSEA_results/plots/DRgenesAmpRatio1_Log(AD-CTL)ranked.png" 
                                     DRgenesAmpRatio1_minusLogPRanked.rnk 
            "../fGSEA_results/plots/DRgenesAmpRatio1_minusLogPRanked.png" 
                          DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.rnk 
 "../fGSEA_results/plots/DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.png" 
                                  DRgenesAmpRatio25_Log(AD-CTL)ranked.rnk 
         "../fGSEA_results/plots/DRgenesAmpRatio25_Log(AD-CTL)ranked.png" 
                            DRgenesAmpRatio25_minusLogPRanked_method2.rnk 
   "../fGSEA_results/plots/DRgenesAmpRatio25_minusLogPRanked_method2.png" 
                                    DRgenesAmpRatio25_minusLogPRanked.rnk 
           "../fGSEA_results/plots/DRgenesAmpRatio25_minusLogPRanked.png" 

Run fgsea on sleep related pathways from https://doi.org/10.1152/physiolgenomics.00275.2006

sleep_wake_pathways = gmtPathways("./MsigDB_gmts_for_GSEA/sleep_wake_pathways_w_all_human_aliases_filtered_to_background_genes.gmt")

if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results_sleep_wake", sep = "/")))){
    dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results_sleep_wake", sep = "/") )
    dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results_sleep_wake", "plots", sep = "/") )
}
setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/fGSEA/rnk_files inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
run_fgsea(rnk_files, gene_remapping_dict, sleep_wake_pathways, dir = "fGSEA_results_sleep_wake", max_size = 10000)
[1] "../fGSEA_results_sleep_wake/AD_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
Saving 7 x 7 in image
[1] "../fGSEA_results_sleep_wake/CTL_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results_sleep_wake/differential_mesor_all_genes_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results_sleep_wake/DRgenesAmpRatio1_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results_sleep_wake/DRgenesAmpRatio1_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results_sleep_wake/DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results_sleep_wake/DRgenesAmpRatio25_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results_sleep_wake/DRgenesAmpRatio25_minusLogPRanked_method2.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results_sleep_wake/DRgenesAmpRatio25_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
                                                      AD_cyclers_minusLogPRanked.rnk 
                  "../fGSEA_results_sleep_wake/plots/AD_cyclers_minusLogPRanked.png" 
                                                     CTL_cyclers_minusLogPRanked.rnk 
                 "../fGSEA_results_sleep_wake/plots/CTL_cyclers_minusLogPRanked.png" 
                                    differential_mesor_all_genes_minusLogPRanked.rnk 
"../fGSEA_results_sleep_wake/plots/differential_mesor_all_genes_minusLogPRanked.png" 
                                              DRgenesAmpRatio1_Log(AD-CTL)ranked.rnk 
          "../fGSEA_results_sleep_wake/plots/DRgenesAmpRatio1_Log(AD-CTL)ranked.png" 
                                                DRgenesAmpRatio1_minusLogPRanked.rnk 
            "../fGSEA_results_sleep_wake/plots/DRgenesAmpRatio1_minusLogPRanked.png" 
                                     DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.rnk 
 "../fGSEA_results_sleep_wake/plots/DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.png" 
                                             DRgenesAmpRatio25_Log(AD-CTL)ranked.rnk 
         "../fGSEA_results_sleep_wake/plots/DRgenesAmpRatio25_Log(AD-CTL)ranked.png" 
                                       DRgenesAmpRatio25_minusLogPRanked_method2.rnk 
   "../fGSEA_results_sleep_wake/plots/DRgenesAmpRatio25_minusLogPRanked_method2.png" 
                                               DRgenesAmpRatio25_minusLogPRanked.rnk 
           "../fGSEA_results_sleep_wake/plots/DRgenesAmpRatio25_minusLogPRanked.png" 

Phase Set Enrichment Analysis (PSEA)

path = getwd()
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

# List of pathways, downloaded from MsigDB, absolute paths
psea_pathways <- c(paste0(getwd(), "/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), paste0(getwd(), "/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))

# make sure no spaces when calling cmd
psea_pathways = gsub(" ", "\\ ", psea_pathways, fixed = TRUE) 

# change dir into PSEA directory
setwd(paste(path_to_cyclops_ordering,"downstream_output", "PSEA_files",sep = "/"))
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/PSEA_files inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
#list PSEA input files (generated during cosinor regression/DR step)
psea_files = list.files(pattern = "*.txt")

#Save path to ordering as string for cleaning up call to system
path_to_cyclops_ordering_no_space = gsub(" ", "\\ ", path_to_cyclops_ordering, fixed = TRUE)

#dataframe where rows are arguments to system, I will apply system call across rows
arg_df = expand.grid(psea_files, psea_pathways) %>% 
      mutate(out_dirs = paste(str_extract(string = as.character(Var1),     pattern= ".+(?=\\.txt)"), basename(as.character(Var2)) %>% str_extract(pattern= ".+(?=\\.gmt)")%>% 
      gsub(pattern = "\\.", replacement = ""), sep = "_") )

#apply system call, calling PSEA jar file, using rows of arg_df as arguments
apply(arg_df, 1, function(a){
    system(paste0("java -jar ", path_no_space, "/PSEA_cmd.jar ", 
    paste0(path_to_cyclops_ordering_no_space, 
    "/downstream_output/PSEA_files/", a[[1]]), " ", a[[2]]," ",
    paste0(path_to_cyclops_ordering_no_space,
    "/downstream_output/PSEA_files/", a[[3]]), " 5 10000 pdf"))
        })
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1_c2cpkeggv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 197 items
Successfully loaded 186 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1_c2cpkeggv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 204 items
Successfully loaded 186 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs_c2cpkeggv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 7 items
Successfully loaded 186 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1_hallv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 197 items
Successfully loaded 50 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1_hallv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 204 items
Successfully loaded 50 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs_hallv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 7 items
Successfully loaded 50 items
[1] 0 0 0 0 0 0

Transcription Factor Analysis

Now I search for transcription factors associated with my various gene lists, i.e, TF’s associated with genes that lose amplitude in AD, etc.

path = getwd()

#create pscan dir if does not exist:
if(!(dir.exists(paste0(path_to_cyclops_ordering, "downstream_output/pscan")))){
  dir.create(paste0(path_to_cyclops_ordering, "downstream_output/pscan") )
}
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
#grab gene lists from enrichR files directory
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|DR_)")

#write pscan input
lapply(gene_lists, write_pscan_input)
Loading required package: AnnotationDbi
Warning: package ‘AnnotationDbi’ was built under R version 4.3.1Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:gridExtra’:

    combine

The following objects are masked from ‘package:lubridate’:

    intersect, setdiff, union

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter,
    Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max,
    which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and
    for packages 'citation("pkgname")'.

Loading required package: IRanges
Warning: package ‘IRanges’ was built under R version 4.3.1Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

    first, second

The following objects are masked from ‘package:lubridate’:

    second, second<-

The following objects are masked from ‘package:dplyr’:

    first, rename

The following object is masked from ‘package:tidyr’:

    expand

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    expand.grid, I, unname


Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

The following object is masked from ‘package:lubridate’:

    %within%

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice

The following object is masked from ‘package:purrr’:

    reduce


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:

    select


'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

[[5]]
NULL

[[6]]
NULL

[[7]]
NULL

[[8]]
NULL

[[9]]
NULL

[[10]]
NULL

[[11]]
NULL

[[12]]
NULL

[[13]]
NULL

[[14]]
NULL

[[15]]
NULL

[[16]]
NULL

[[17]]
NULL

[[18]]
NULL

[[19]]
NULL

[[20]]
NULL
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

setwd("pscan/")
pscan_files = list.files("./pscan_files/", pattern = ".csv$")

sapply(pscan_files, function(x){
  system(paste0("python3 ", path_no_space, "/pscan_requests.py --file pscan_files/" ,x))})
Finished Pscan on AD_CTL_mthd2_cyclers_AR25BHQ1_pscan.csv
Number of genes: 566
Finished Pscan on AD_cyclers_AR25BHQ1_pscan.csv
Number of genes: 340
Finished Pscan on AD_cyclers_AR33BHQ1_pscan.csv
Number of genes: 137
Finished Pscan on CTL_cyclers_AR25BHQ1_pscan.csv
Number of genes: 382
Finished Pscan on CTL_cyclers_AR33BHQ1_pscan.csv
Number of genes: 150
AD_CTL_mthd2_cyclers_AR25BHQ1_pscan.csv           AD_cyclers_AR25BHQ1_pscan.csv           AD_cyclers_AR33BHQ1_pscan.csv 
                                      0                                       0                                       0 
         CTL_cyclers_AR25BHQ1_pscan.csv          CTL_cyclers_AR33BHQ1_pscan.csv 
                                      0                                       0 
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

if(exists("deseq_de_filename")){
  setwd("pscan_results")
  pscan_result_files = list.files(pattern = ".csv$")
  print("Searching cycling and DR results for pscan TF")
  sapply(pscan_result_files, augment_tf_file, deseq_de_filename, isCyclingBHQCutoff_str)
  setwd(paste0(path_to_cyclops_ordering, "downstream_output/enrichR_results"))
  directories = list.files()
  enrichR_TF_paths <- lapply(directories, function(dir) list.files(dir, full.names = TRUE, recursive = TRUE, pattern = ".*TRANSFACandJASPARPWMs_BCKGRND.*\\.csv|.*TranscriptionFactorPPIs_BCKGRND.*\\.csv"))
  enrichR_TF_paths = flatten(enrichR_TF_paths) %>% paste0("./", .)  
  sapply(enrichR_TF_paths, augment_tf_file, deseq_de_filename,     isCyclingBHQCutoff_str)
  
}
[1] "Searching cycling and DR results for pscan TF"
                                                                                                                                                                                                                                                                                                                                                                             ./EnrichR_ADCTLmthd2cyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADCTLmthd2cyclersAR25BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground.csv 
                                                                  "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_ADCTLmthd2cyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADCTLmthd2cyclersAR25BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                               ./EnrichR_ADCTLmthd2cyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADCTLmthd2cyclersAR25BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground.csv 
                                                                    "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_ADCTLmthd2cyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADCTLmthd2cyclersAR25BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                             ./EnrichR_ADcyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR25BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground.csv 
                                                                                  "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_ADcyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR25BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                               ./EnrichR_ADcyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR25BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground.csv 
                                                                                    "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_ADcyclersAR25BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR25BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                             ./EnrichR_ADcyclersAR33BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR33BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground.csv 
                                                                                  "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_ADcyclersAR33BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR33BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                               ./EnrichR_ADcyclersAR33BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR33BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground.csv 
                                                                                    "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_ADcyclersAR33BHQ1_BCKGRND-EnrichRbackground/ADcyclersAR33BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                           ./EnrichR_CTLcyclersAR25BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR25BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground.csv 
                                                                                "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_CTLcyclersAR25BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR25BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                             ./EnrichR_CTLcyclersAR25BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR25BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground.csv 
                                                                                  "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_CTLcyclersAR25BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR25BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                           ./EnrichR_CTLcyclersAR33BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR33BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground.csv 
                                                                                "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_CTLcyclersAR33BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR33BHQ1_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                             ./EnrichR_CTLcyclersAR33BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR33BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground.csv 
                                                                                  "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_CTLcyclersAR33BHQ1_BCKGRND-EnrichRbackground/CTLcyclersAR33BHQ1_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                   ./EnrichR_diffmesorallgenesBHQ05_BCKGRND-EnrichRbackground/diffmesorallgenesBHQ05_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground.csv 
                                                                        "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_diffmesorallgenesBHQ05_BCKGRND-EnrichRbackground/diffmesorallgenesBHQ05_LIBRY-TranscriptionFactorPPIs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                                                                     ./EnrichR_diffmesorallgenesBHQ05_BCKGRND-EnrichRbackground/diffmesorallgenesBHQ05_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground.csv 
                                                                          "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_diffmesorallgenesBHQ05_BCKGRND-EnrichRbackground/diffmesorallgenesBHQ05_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-EnrichRbackground_plots" 
                                                                                                                                                                                                                                                                                                                                       ./EnrichR_DRcyclersCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25/DRcyclersCyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25.csv 
                            "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_DRcyclersCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25/DRcyclersCyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25_plots" 
                                                                                                                                                                                                                                                                                                               ./EnrichR_DRcyclersmthd2CyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25/DRcyclersmthd2CyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25.csv 
    "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_DRcyclersmthd2CyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25/DRcyclersmthd2CyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25_plots" 
                                                                                                                                                                                                                                                                                                                                   ./EnrichR_DRgainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25/DRgainAmpADCyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25.csv 
                        "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25/DRgainAmpADCyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25_plots" 
                                                                                                                                                                                                                                                                                                           ./EnrichR_DRmthd2gainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25/DRmthd2gainAmpADCyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25.csv 
"/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/enrichR_results/EnrichR_DRmthd2gainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25/DRmthd2gainAmpADCyclingBHQ1AR25DRBHQ2_LIBRY-TRANSFACandJASPARPWMs_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25_plots" 

Write KEGG Files

Write Files for Kegg Pathway Diagrams

entrez_dict = readxl::read_excel("scROSMAP_ENSEMBL_ENTREZ_dict.xlsx")

setwd(path_to_cyclops_ordering)
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

if (!(dir.exists("downstream_output/KEGG_map_diagrams"))){
  dir.create("downstream_output/KEGG_map_diagrams")
}
write_kegg_map_files(paste0("downstream_output/diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio25.csv"),"Log_AD_CTL_ampRatio", trans_dict = entrez_dict,BHQ_cutoff = 0.2)

Metabolon

if (!(dir.exists(paste0(path_to_cyclops_ordering, "/downstream_output/metabolon")))){
  dir.create(paste0(path_to_cyclops_ordering, "/downstream_output/metabolon"))
}

order_metabolon(metabolon_filename, metabolon_datakey, path_to_rosmap_clin, path_to_cyclops_ordering)

Running is_cycling() on cond_subset: cond_0
Running is_cycling() on cond_subset: cond_1
Running is_cycling_method2() (analogue of compareRhythms) on all subjects
Running diff_rhyth() on seedlist of size: 263
Running diff_rhyth() on seedlist of size: 292[[1]]
[1] "plots/100002284_gene_trace.png"

[[2]]
[1] "plots/100000265_gene_trace.png"

[[3]]
[1] "plots/100002458_gene_trace.png"

[[4]]
[1] "plots/799_gene_trace.png"

[[5]]
[1] "plots/100000265_gene_trace.png"

[[6]]
[1] "plots/460_gene_trace.png"

Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/metabolon inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.

Proteomics

Make sure you have downloaded syn32835854, syn21266449, and syn51389605. You can download programmatically with python or R synapse client. Make sure you specify the path to those downloads with proteiomics_file_path.

proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

#make sure you have downloaded syn32835854,  syn21266449, and syn51389605
if (!(dir.exists(paste0(path_to_cyclops_ordering, "/downstream_output/proteomics")))){
  dir.create(paste0(path_to_cyclops_ordering, "/downstream_output/proteomics"))
}

order_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering)
New names:New names:

Running is_cycling() on cond_subset: cond_0

[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running is_cycling() on cond_subset: cond_1

[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running is_cycling_method2() (analogue of compareRhythms) on all subjects

[>----------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running Mesor_differences()

[>----------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>---------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>--------------------------------------------------------------------------------------------------------------------------------------]   3%
[===>-------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>-----------------------------------------------------------------------------------------------------------------------------------]   5%
[======>----------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>---------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   6%
[========>--------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>-------------------------------------------------------------------------------------------------------------------------------]   8%
[==========>------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   8%
[===========>-----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]   9%
[============>----------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  10%
[=============>---------------------------------------------------------------------------------------------------------------------------]  11%
[==============>--------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  11%
[===============>-------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  12%
[================>------------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  13%
[=================>-----------------------------------------------------------------------------------------------------------------------]  14%
[==================>----------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  14%
[===================>---------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  15%
[====================>--------------------------------------------------------------------------------------------------------------------]  16%
[=====================>-------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  16%
[======================>------------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  17%
[=======================>-----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  18%
[========================>----------------------------------------------------------------------------------------------------------------]  19%
[=========================>---------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  19%
[==========================>--------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  20%
[===========================>-------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  21%
[============================>------------------------------------------------------------------------------------------------------------]  22%
[=============================>-----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  22%
[==============================>----------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  23%
[===============================>---------------------------------------------------------------------------------------------------------]  24%
[================================>--------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  24%
[=================================>-------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  25%
[==================================>------------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  26%
[===================================>-----------------------------------------------------------------------------------------------------]  27%
[====================================>----------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  27%
[=====================================>---------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  28%
[======================================>--------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  29%
[=======================================>-------------------------------------------------------------------------------------------------]  30%
[========================================>------------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  30%
[=========================================>-----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  31%
[==========================================>----------------------------------------------------------------------------------------------]  32%
[===========================================>---------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  32%
[============================================>--------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  33%
[=============================================>-------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  34%
[==============================================>------------------------------------------------------------------------------------------]  35%
[===============================================>-----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  35%
[================================================>----------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  36%
[=================================================>---------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  37%
[==================================================>--------------------------------------------------------------------------------------]  38%
[===================================================>-------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  38%
[====================================================>------------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  39%
[=====================================================>-----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  40%
[======================================================>----------------------------------------------------------------------------------]  41%
[=======================================================>---------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  41%
[========================================================>--------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  42%
[=========================================================>-------------------------------------------------------------------------------]  43%
[==========================================================>------------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  43%
[===========================================================>-----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  44%
[============================================================>----------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  45%
[=============================================================>---------------------------------------------------------------------------]  46%
[==============================================================>--------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  46%
[===============================================================>-------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  47%
[================================================================>------------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  48%
[=================================================================>-----------------------------------------------------------------------]  49%
[==================================================================>----------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  49%
[===================================================================>---------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  50%
[====================================================================>--------------------------------------------------------------------]  51%
[=====================================================================>-------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  51%
[======================================================================>------------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  52%
[=======================================================================>-----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  53%
[========================================================================>----------------------------------------------------------------]  54%
[=========================================================================>---------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  54%
[==========================================================================>--------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  55%
[===========================================================================>-------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  56%
[============================================================================>------------------------------------------------------------]  57%
[=============================================================================>-----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  57%
[==============================================================================>----------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  58%
[===============================================================================>---------------------------------------------------------]  59%
[================================================================================>--------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  59%
[=================================================================================>-------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  60%
[==================================================================================>------------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  61%
[===================================================================================>-----------------------------------------------------]  62%
[====================================================================================>----------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  62%
[=====================================================================================>---------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  63%
[======================================================================================>--------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  64%
[=======================================================================================>-------------------------------------------------]  65%
[========================================================================================>------------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  65%
[=========================================================================================>-----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  66%
[==========================================================================================>----------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  67%
[===========================================================================================>---------------------------------------------]  68%
[============================================================================================>--------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  68%
[=============================================================================================>-------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  69%
[==============================================================================================>------------------------------------------]  70%
[===============================================================================================>-----------------------------------------]  70%
[================================================================================================>----------------------------------------]  70%
[================================================================================================>----------------------------------------]  71%
[=================================================================================================>---------------------------------------]  71%
[=================================================================================================>---------------------------------------]  72%
[==================================================================================================>--------------------------------------]  72%
[==================================================================================================>--------------------------------------]  73%
[===================================================================================================>-------------------------------------]  73%
[====================================================================================================>------------------------------------]  73%
[====================================================================================================>------------------------------------]  74%
[=====================================================================================================>-----------------------------------]  74%
[=====================================================================================================>-----------------------------------]  75%
[======================================================================================================>----------------------------------]  75%
[======================================================================================================>----------------------------------]  76%
[=======================================================================================================>---------------------------------]  76%
[========================================================================================================>--------------------------------]  76%
[========================================================================================================>--------------------------------]  77%
[=========================================================================================================>-------------------------------]  77%
[=========================================================================================================>-------------------------------]  78%
[==========================================================================================================>------------------------------]  78%
[===========================================================================================================>-----------------------------]  78%
[===========================================================================================================>-----------------------------]  79%
[============================================================================================================>----------------------------]  79%
[============================================================================================================>----------------------------]  80%
[=============================================================================================================>---------------------------]  80%
[=============================================================================================================>---------------------------]  81%
[==============================================================================================================>--------------------------]  81%
[===============================================================================================================>-------------------------]  81%
[===============================================================================================================>-------------------------]  82%
[================================================================================================================>------------------------]  82%
[================================================================================================================>------------------------]  83%
[=================================================================================================================>-----------------------]  83%
[=================================================================================================================>-----------------------]  84%
[==================================================================================================================>----------------------]  84%
[===================================================================================================================>---------------------]  84%
[===================================================================================================================>---------------------]  85%
[====================================================================================================================>--------------------]  85%
[====================================================================================================================>--------------------]  86%
[=====================================================================================================================>-------------------]  86%
[======================================================================================================================>------------------]  86%
[======================================================================================================================>------------------]  87%
[=======================================================================================================================>-----------------]  87%
[=======================================================================================================================>-----------------]  88%
[========================================================================================================================>----------------]  88%
[========================================================================================================================>----------------]  89%
[=========================================================================================================================>---------------]  89%
[==========================================================================================================================>--------------]  89%
[==========================================================================================================================>--------------]  90%
[===========================================================================================================================>-------------]  90%
[===========================================================================================================================>-------------]  91%
[============================================================================================================================>------------]  91%
[============================================================================================================================>------------]  92%
[=============================================================================================================================>-----------]  92%
[==============================================================================================================================>----------]  92%
[==============================================================================================================================>----------]  93%
[===============================================================================================================================>---------]  93%
[===============================================================================================================================>---------]  94%
[================================================================================================================================>--------]  94%
[================================================================================================================================>--------]  95%
[=================================================================================================================================>-------]  95%
[==================================================================================================================================>------]  95%
[==================================================================================================================================>------]  96%
[===================================================================================================================================>-----]  96%
[===================================================================================================================================>-----]  97%
[====================================================================================================================================>----]  97%
[=====================================================================================================================================>---]  97%
[=====================================================================================================================================>---]  98%
[======================================================================================================================================>--]  98%
[======================================================================================================================================>--]  99%
[=======================================================================================================================================>-]  99%
[=======================================================================================================================================>-] 100%
[========================================================================================================================================>] 100%
[=========================================================================================================================================] 100%
                                                                                                                                                

Running diff_rhyth() on seedlist of size: 753
Running diff_rhyth() on seedlist of size: 942[[1]]
[1] "plots/KIF5A|Q12840_gene_trace.png"

[[2]]
[1] "plots/RPS6KA5|O75582_gene_trace.png"

[[3]]
[1] "plots/FKBP5|Q13451_gene_trace.png"

[[4]]
[1] "plots/BOLA2; BOLA2B|Q9H3K6_gene_trace.png"

[[5]]
[1] "plots/OXSR1|O95747_gene_trace.png"

[[6]]
[1] "plots/PEX11B|O96011_gene_trace.png"

Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/downstream_output/proteomics inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.

Plot Other Proteins

plot_list = c("BPNT1|O95861", "PPM1B|O75688", "BLVRA|P53004", "HDHD2|Q9H0R4")

proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

plot_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering, c("RPL10|P27635", "RPL32|P62910", "NDUFB1|O75438"), percentile = percentile)

fGSEA on proteomics

path = getwd()
setwd(path_to_cyclops_ordering)
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
if (!(dir.exists("downstream_output/proteomics/fGSEA"))){
  dir.create("downstream_output/proteomics/fGSEA")
  dir.create("downstream_output/proteomics/fGSEA/rnk_files")
  dir.create("downstream_output/proteomics/fGSEA/fGSEA_results")
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#path of parent folder
setwd(path)

write_prot_rnks(path_to_cyclops_ordering)
[1] "Creating rnk files for fGSEA."
#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_UniProt_IDs_MSigDB.v2023.2.Hs.chip", sep = '\t')

setwd(paste0(path_to_cyclops_ordering,"/downstream_output/proteomics/fGSEA/rnk_files"))

rnk_files = list.files(pattern = ".rnk")

run_fgsea(rnk_files, gene_remapping_dict, pathways)
[1] "../fGSEA_results/AD_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
Saving 7 x 7 in image
[1] "../fGSEA_results/CTL_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/diff_mesor_(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DR_cyclers_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DR_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
                           AD_cyclers_minusLogPRanked.rnk                           CTL_cyclers_minusLogPRanked.rnk 
  "../fGSEA_results/plots/AD_cyclers_minusLogPRanked.png"  "../fGSEA_results/plots/CTL_cyclers_minusLogPRanked.png" 
                            diff_mesor_(AD-CTL)ranked.rnk                          DR_cyclers_Log(AD-CTL)ranked.rnk 
   "../fGSEA_results/plots/diff_mesor_(AD-CTL)ranked.png" "../fGSEA_results/plots/DR_cyclers_Log(AD-CTL)ranked.png" 
                           DR_cyclers_minusLogPRanked.rnk 
  "../fGSEA_results/plots/DR_cyclers_minusLogPRanked.png" 
---
title: "Perform Downstream Analysis"
output: html_notebook
editor_options: 
  chunk_output_type: inline
---

This notebook is for performing downstream analysis of CYCLOPS. It includes running cosinor regression and assessing differential rhythmicity (two ways for both), calling the enrichR API via python, using fgsea in R, running PSEA, outputing files for making KEGG map diagrams, etc.

### Load Packages

```{r Load Libraries, include=FALSE}
library(reticulate) #use to find conda env for python
library(tidyverse)
library(JuliaCall)
julia = julia_setup("/Applications/Julia-1.6.app/Contents/Resources/julia/bin/")
source("./differential_rhyth_generalized.R")
source("./create_rnk_files.R")
source("./fgsea.R")
source("./Mesor_Venn_Diagram.R")
source("./Files_for_Pscan.R")
source("./Make_KEGG_map_files.R")
source("./Check_TF_for_cycling_or_DR.R")
source("./fgsea_plot_for_downstream.R")
source("./plot_clock_face_plots.R")
source("./plot_gene_traces_generalized.R")
source("./order_metabolon.R")
source("./order_proteomics.R")
```

This notebook makes use of python via anaconda. Please make sure you install anaconda to proceed:

```{r}
conda_list()
```

Select your conda environment of choice, in my case, item 2 from list above:

```{r}
conda_list()[[2]][2] %>% 
  use_condaenv(required = TRUE)
print(paste("Using cond env:",conda_list()[[1]][2] ))
```

### Setup

Select the CYCLOPS ordering path and path to data file and path to DEseq2 differential expression results:

```{r}
#path to cyclops ordering
path_to_cyclops_ordering = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit_Feb5Redo/"

#path to normalized counts
path_to_tmm_file = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/tmms/scROSMAP/cogdx_controls/EdgeR_filt_normed/Microglia_4_5_6_7_8_10_11_13_15_16_FiltByExprDefault_TMM.csv"

# optional path to file containing differential expression results
deseq_de_filename = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/simple_differential_expr/Mglia_4_5_6_7_8_10_11_13_15_16/ Microglia_4_5_6_7_8_10_11_13_15_16_filtByExpr_combatSeq_edgeR_DE_exactTest.csv"

path_to_rosmap_clin = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Meta_data/cleaned_rosmap_meta_cogdxConds.csv"
metabolon_filename = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Brain514_assay_data.csv"
metabolon_datakey = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Data_Dictionary.csv"

#BHQ corrected p cutoff to be considered cycling in analysis:
isCyclingBHQCutoff = 0.1
percentile = 0.025
useBatch = T
```

### Cosinor Regression and Differential Rhythmicity

Run cosinor regression and differential rhythmicity analysis with custom script and with compareRhythms library. I make use of Ensembl and Entrez IDs so I need the following translation dictionaries:

```{r}
# read in translation dict between gene symbols and other alias
Ensembl_dict = readxl::read_xlsx("scROSMAP_ENSEMBL_dict.xlsx")

#run custom cycling and differential rhythmicity analysis
print("***Running cosinor and differential rhythms analysis***")
run_cycling_and_dr_analysis(path_to_cyclops_ordering, path_to_tmm_file, isCyclingSigCutoff = isCyclingBHQCutoff, percentile = percentile, useBatch = useBatch)
```

### Plotting

With custom regression, I have to remake clock face plots, genes plots, etc.

```{r}
setwd(path_to_cyclops_ordering)
if (!(dir.exists("downstream_output/plots"))){
  dir.create("downstream_output/plots")
}

#for cycling_in_CTL.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/CTL_clock_face_plot.png"), "downstream_output/cosinor_results_CTL.csv", mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0, force_align = 5.907, force_flipped = T)

setwd(path_to_cyclops_ordering)

#for cycling_in_AD.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/AD_clock_face_plot.png"),"downstream_output/cosinor_results_AD.csv",mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0, force_align = 5.907, force_flipped = T)

#plot cyclops histogram
plot_subject_histogram(path_to_cyclops_ordering, "cond_0")
plot_subject_histogram(path_to_cyclops_ordering, "cond_1")

#Gene Tracings
plot_core_clock_genes(path_to_tmm_file, path_to_cyclops_ordering, useBatch = useBatch, percentile = percentile, split_cond_plots = T)
```

Plot Other Genes

```{r}
plot_me = c("RPL18","RPS7","RPL22","RPS18","RPL8","RPL10A","RPS13","RPL14","RPS15A","RPS12","RPL36AL","RPL34","RPL30","RPL9","RPL21","RPS28","RPSA","RPL26","RPL27A","FAU","RPS3A","RPL7A","RPL17","RPS27A","RPS16","RPL15","RPLP1","RPL7","RPL10","RPL23A","RPL18A","RPL3","RPL12","RPL39","RPL37A","RPL37","RPS10","RPL13","RPL35A","RPS23","RPL13A","RPL38","RPS29","RPL24","RPL41","RPL35","RPS26","RPS2","RPS9","RPL32","RPL6","RPS21","RPS24","RPS25","RPL36","RPL19","RPS27","RPL29","RPS15","RPS3","RPS5","RPS8","RPL27","RSL24D1","RPS6","RPL11")

tmm = read_csv(path_to_tmm_file, show_col_types = FALSE)
  cyc_pred_file = list.files(path = paste0(path_to_cyclops_ordering, "/Fits/"), pattern = '*Fit_Output_*')
cyc_pred = read_csv(paste(path_to_cyclops_ordering, "Fits", cyc_pred_file[1], sep = '/'), show_col_types = FALSE)
plot_gene_trace(cyc_pred, tmm, plot_me , percentile = percentile, useBatch = useBatch)
```

### EnrichR

Call EnrichR API with python, supplying various lists from cycling and differential rhythm analysis.

```{r}
path = getwd()
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)
#create list of filenames from the enrichR_files subfolder
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|diff_mesor)")

#run system command to call python script that uses enrichR API
sapply(gene_lists, function(x){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"enrichR_files/EnrichR_background.csv\""))})

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

setwd("enrichR_files/")
all_DR_gene_lists = list.files( pattern = "^(DR_)")
method2_files = grepl("mthd2", all_DR_gene_lists)
DR_gene_lists_method1 = all_DR_gene_lists[!method2_files]
DR_backgrounds_method1 = paste0("diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method1, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists_method2 = all_DR_gene_lists[method2_files]
DR_backgrounds_method2 = paste0("diff_rhythms_method2_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method2, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists = c(DR_gene_lists_method1, DR_gene_lists_method2)
DR_backgrounds = c(DR_backgrounds_method1, DR_backgrounds_method2)

# repeat with differential gene lists
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
mapply(function(x, y){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"",y , "\""))},
  DR_gene_lists, 
  DR_backgrounds)

#AD severity
system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/strong_cogdx_diffs_AR25.csv\" -b \"enrichR_files/AD_cyclers_AR25BHQ05.csv\""))
```

### FGSEA

```{r}
path = getwd()
setwd(path_to_cyclops_ordering)
if (!(dir.exists("downstream_output/fGSEA"))){
  dir.create("downstream_output/fGSEA")
  dir.create(paste("downstream_output", "fGSEA", "rnk_files", sep = "/"))
  dir.create(paste("downstream_output" , "fGSEA", "fGSEA_results", sep = "/"))
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#create rnk files
write_rnks(path_to_cyclops_ordering, isCyclingBHQCutoff_str)

#path of parent folder
setwd(path)

#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_Gene_Symbol_with_Remapping_MSigDB.v2023.1.Hs.chip", sep = '\t')

setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))

rnk_files = list.files(pattern = ".rnk")


if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results", sep = "/")))){
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", sep = "/") )
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", "plots",sep = "/"))
}

run_fgsea(rnk_files, gene_remapping_dict, pathways)
```

Run fgsea on sleep related pathways from https://doi.org/10.1152/physiolgenomics.00275.2006

```{r}
sleep_wake_pathways = gmtPathways("./MsigDB_gmts_for_GSEA/sleep_wake_pathways_w_all_human_aliases_filtered_to_background_genes.gmt")

if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results_sleep_wake", sep = "/")))){
    dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results_sleep_wake", sep = "/") )
    dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results_sleep_wake", "plots", sep = "/") )
}
setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))

run_fgsea(rnk_files, gene_remapping_dict, sleep_wake_pathways, dir = "fGSEA_results_sleep_wake", max_size = 10000)
```

### Phase Set Enrichment Analysis (PSEA)

```{r}
path = getwd()
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

# List of pathways, downloaded from MsigDB, absolute paths
psea_pathways <- c(paste0(getwd(), "/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), paste0(getwd(), "/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))

# make sure no spaces when calling cmd
psea_pathways = gsub(" ", "\\ ", psea_pathways, fixed = TRUE) 

# change dir into PSEA directory
setwd(paste(path_to_cyclops_ordering,"downstream_output", "PSEA_files",sep = "/"))

#list PSEA input files (generated during cosinor regression/DR step)
psea_files = list.files(pattern = "*.txt")

#Save path to ordering as string for cleaning up call to system
path_to_cyclops_ordering_no_space = gsub(" ", "\\ ", path_to_cyclops_ordering, fixed = TRUE)

#dataframe where rows are arguments to system, I will apply system call across rows
arg_df = expand.grid(psea_files, psea_pathways) %>% 
      mutate(out_dirs = paste(str_extract(string = as.character(Var1),     pattern= ".+(?=\\.txt)"), basename(as.character(Var2)) %>% str_extract(pattern= ".+(?=\\.gmt)")%>% 
      gsub(pattern = "\\.", replacement = ""), sep = "_") )

#apply system call, calling PSEA jar file, using rows of arg_df as arguments
apply(arg_df, 1, function(a){
    system(paste0("java -jar ", path_no_space, "/PSEA_cmd.jar ", 
    paste0(path_to_cyclops_ordering_no_space, 
    "/downstream_output/PSEA_files/", a[[1]]), " ", a[[2]]," ",
    paste0(path_to_cyclops_ordering_no_space,
    "/downstream_output/PSEA_files/", a[[3]]), " 5 10000 pdf"))
        })
```

### 

### Transcription Factor Analysis

Now I search for transcription factors associated with my various gene lists, i.e, TF's associated with genes that lose amplitude in AD, etc.

```{r}
path = getwd()

#create pscan dir if does not exist:
if(!(dir.exists(paste0(path_to_cyclops_ordering, "downstream_output/pscan")))){
  dir.create(paste0(path_to_cyclops_ordering, "downstream_output/pscan") )
}
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))

#grab gene lists from enrichR files directory
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|DR_)")

#write pscan input
lapply(gene_lists, write_pscan_input)
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

setwd("pscan/")
pscan_files = list.files("./pscan_files/", pattern = ".csv$")

sapply(pscan_files, function(x){
  system(paste0("python3 ", path_no_space, "/pscan_requests.py --file pscan_files/" ,x))})

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

if(exists("deseq_de_filename")){
  setwd("pscan_results")
  pscan_result_files = list.files(pattern = ".csv$")
  print("Searching cycling and DR results for pscan TF")
  sapply(pscan_result_files, augment_tf_file, deseq_de_filename, isCyclingBHQCutoff_str)
  setwd(paste0(path_to_cyclops_ordering, "downstream_output/enrichR_results"))
  directories = list.files()
  enrichR_TF_paths <- lapply(directories, function(dir) list.files(dir, full.names = TRUE, recursive = TRUE, pattern = ".*TRANSFACandJASPARPWMs_BCKGRND.*\\.csv|.*TranscriptionFactorPPIs_BCKGRND.*\\.csv"))
  enrichR_TF_paths = flatten(enrichR_TF_paths) %>% paste0("./", .)  
  sapply(enrichR_TF_paths, augment_tf_file, deseq_de_filename,     isCyclingBHQCutoff_str)
  
}
```

### Write KEGG Files

Write Files for Kegg Pathway Diagrams

```{r}
entrez_dict = readxl::read_excel("scROSMAP_ENSEMBL_ENTREZ_dict.xlsx")

setwd(path_to_cyclops_ordering)
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

if (!(dir.exists("downstream_output/KEGG_map_diagrams"))){
  dir.create("downstream_output/KEGG_map_diagrams")
}
write_kegg_map_files(paste0("downstream_output/diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio25.csv"),"Log_AD_CTL_ampRatio", trans_dict = entrez_dict,BHQ_cutoff = 0.2)

```

### Metabolon

```{r}
if (!(dir.exists(paste0(path_to_cyclops_ordering, "/downstream_output/metabolon")))){
  dir.create(paste0(path_to_cyclops_ordering, "/downstream_output/metabolon"))
}

order_metabolon(metabolon_filename, metabolon_datakey, path_to_rosmap_clin, path_to_cyclops_ordering)
```

### Proteomics

Make sure you have downloaded [**syn32835854**]{.underline}, [**syn21266449**]{.underline}, and [**syn51389605**]{.underline}. You can download programmatically with python or R synapse client. Make sure you specify the path to those downloads with *proteiomics_file_path.*

```{r}
proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

#make sure you have downloaded syn32835854,  syn21266449, and syn51389605
if (!(dir.exists(paste0(path_to_cyclops_ordering, "/downstream_output/proteomics")))){
  dir.create(paste0(path_to_cyclops_ordering, "/downstream_output/proteomics"))
}

order_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering)
```

Plot Other Proteins

```{r}
plot_list = c("BPNT1|O95861", "PPM1B|O75688", "BLVRA|P53004", "HDHD2|Q9H0R4")

proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

plot_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering, c("RPL10|P27635", "RPL32|P62910", "NDUFB1|O75438"), percentile = percentile)
```

fGSEA on proteomics

```{r}
path = getwd()
setwd(path_to_cyclops_ordering)
if (!(dir.exists("downstream_output/proteomics/fGSEA"))){
  dir.create("downstream_output/proteomics/fGSEA")
  dir.create("downstream_output/proteomics/fGSEA/rnk_files")
  dir.create("downstream_output/proteomics/fGSEA/fGSEA_results")
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#path of parent folder
setwd(path)

write_prot_rnks(path_to_cyclops_ordering)

#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_UniProt_IDs_MSigDB.v2023.2.Hs.chip", sep = '\t')

setwd(paste0(path_to_cyclops_ordering,"/downstream_output/proteomics/fGSEA/rnk_files"))

rnk_files = list.files(pattern = ".rnk")

run_fgsea(rnk_files, gene_remapping_dict, pathways)
```
